Chromosome abnormalities are often associated with genetic disorders, degenerative diseases, and cancer. In particular, the deletion or multiplication of copies of whole chromosomes or chromosomal segments, and higher level amplifications of specific regions of the genome are common occurrences in cancer. See, for example Smith, et al., Breast Cancer Res. Treat., 18: Suppl. 1:5-14 (1991, van de Vijer & Nusse, Biochim. Biophys. Acta. 1072:33-50 (1991), Sato, et al., Cancer. Res., 50: 7184-7189 (1990). In fact, the amplification and deletion of DNA sequences containing protooncogenes and tumor-suppressor genes, respectively, are frequently characteristic of tumorigenesis. Dutrillaux, et al., Cancer Genet. Cytogenet., 49:203-217 (1990). Clearly the identification of amplified and deleted regions and the cloning of the genes involved is crucial both to the study of tumorigenesis and to the development of cancer diagnostics.
The detection of amplified or deleted chromosomal regions has traditionally been done by cytogenetics. Because of the complex packing of DNA into the chromosomes, resolution of cytogenetic techniques has been limited to regions larger than about 10 Mb; approximately the width of a band in Giemsa-stained chromosomes. In complex karyotypes with multiple translocations and other genetic changes, traditional cytogenetic analysis is of little utility because karyotype information is lacking or cannot be interpreted. Teyssier, J. R., Cancer Genet. Cytogenet., 37:103 (1989). Furthermore conventional cytogenetic banding analysis is time consuming, labor intensive, and frequently difficult or impossible.
More recently, cloned probes have been used to assess the amount of a given DNA sequence in a chromosome by Southern blotting. This method is effective even if the genome is heavily rearranged so as to eliminate useful karyotype information. However, Southern blotting only gives a rough estimate of the copy number of a DNA sequence, and does not give any information about the localization of that sequence within the chromosome.
Comparative genomic hybridization (CGH) is a more recent approach to identify the presence and localization of amplified/deleted sequences. See Kallioniemi, et al., Science, 258:818 (1992). CGH, like Southern blotting, reveals amplifications and deletions irrespective of genome rearrangement. Additionally, CGH provides a more quantitative estimate of copy number than Souther blotting , and moreover also provides information of the localization of the amplified or deleted sequence in the normal chromosome.
Generally, where detection of deletions or amplifications is limited to the loss or gain of one copy of a sequence, the resolution of prior art methods may be limited. New techniques which provide increased sensitivity, more precise localization of the affected DNA sequence, and more quantitative estimate of copy number, even in samples of mixed normal and tumor cells is particularly desirable. The present invention provides these and other benefits.